Article
Genetics & Heredity
Alia Ebrahim, Manal A. Alfwuaires, Mohammad H. Abukhalil, Fawaz Alasmari, Fawad Ahmad, Rui Yao, Ying Luo, Ying Huang
Summary: This study used bioinformatics analysis to investigate the role of three genes, spGrx4, spFep1, and spPhp4, in maintaining iron homeostasis in the fission yeast Schizosaccharomyces pombe. Multiple sequence alignment and protein-protein interaction analysis provided insights into their similarities with sequence homologs in other species and their cooperative roles in iron homeostasis.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Yusuke Oizumi, Takuto Kaji, Sanki Tashiro, Yumiko Takeshita, Yuko Date, Junko Kanoh
Summary: The complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe were reported, revealing highly polymorphic and hot spots for genome variation features. These subtelomeric regions may contribute to genome diversity and potentially lead to various diseases.
NATURE COMMUNICATIONS
(2021)
Review
Biotechnology & Applied Microbiology
R. Sahaya Glingston, Jyoti Yadav, Jitika Rajpoot, Neha Joshi, Shirisha Nagotu
Summary: Yeast has been proven to be a valuable model system for studying viral infection and expression of viral proteins, advancing our understanding of important viruses. Through high-throughput analysis, genetic manipulation, and its compact genome, yeast provides insights into various aspects related to virus replication.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Hokuto Ohtsuka, Takafumi Shimasaki, Hirofumi Aiba
Summary: Studies have shown that sulfur plays essential roles in biological molecules and different yeast models exhibit varying sulfur metabolism pathways. Sulfur starvation induces various cellular responses in fission yeast, contributing to a better understanding of stress and lifespan regulation caused by sulfur depletion.
FEMS YEAST RESEARCH
(2021)
Review
Microbiology
Hokuto Ohtsuka, Kazuki Imada, Takafumi Shimasaki, Hirofumi Aiba
Summary: The fission yeast S. pombe adapts to the environment and survives in nutrient-starved conditions through sexual differentiation and extension of the chronological lifespan. Spore formation in S. pombe is highly resistant to stresses and spores can survive for a long period. This minireview focuses on the molecular mechanisms of spore formation induced by starvation and highlights the presence of an effective survival mechanism.
Review
Microbiology
Rui Yao, Rongrong Li, Ying Huang
Summary: This review discusses the molecular mechanisms of maintaining zinc homeostasis in Schizosaccharomyces pombe. The transcription factor Loz1 plays a key role in regulating zinc acquisition genes and the transport of excess zinc. When zinc levels are limited, Loz1 is inactivated and zinc is released from the secretory pathway for cellular use.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Barbara Sivakova, Jan Jurcik, Veronika Lukacova, Tomas Selicky, Ingrid Cipakova, Peter Barath, Lubos Cipak
Summary: The LFQ phosphoproteomics workflow presented in this study, based on sequential Fe-IMAC phosphopeptide enrichment, strong anion exchange (SAX), and porous graphitic carbon (PGC) fractionation strategies, enabled the identification of 8353 phosphosites in the fission yeast Schizosaccharomyces pombe, with 1274 sites being newly discovered. The results demonstrate that the combination of PGC and SAX fractionation strategies significantly enhances the robustness and specificity of LFQ phosphoproteomics studies, providing valuable insights into the complexity of protein kinase functions in S. pombe.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Shane Chen, Maria Lyanguzova, Ross Kaufhold, Karen M. Plevock Haase, Hangnoh Lee, Alexei Arnaoutov, Mary Dasso
Summary: The localization of RanGAP to the nuclear envelope is widely conserved in multicellular organisms, but the specific targeting mechanisms vary. In Drosophila, it was found that RanGAP requires binding to a specific nucleoporin for its function and plays a crucial role in pupal development.
Article
Environmental Sciences
Alica Navratilova, Marek Kovar, Miroslava Pozgajova
Summary: Cadmium induces cell shape alterations and growth impairment, while ascorbic acid improves cell condition under cadmium stress at appropriate concentrations, caution is needed for its potential pro-oxidant activity at overdose.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Stephen R. Hennigar, Cassandra Olson, Alyssa M. Kelley, James P. McClung
Summary: This study investigated the expression of zinc transporters in the small intestine of mice and found that Slc39a4 is positively associated with the appearance of Zn-67 in the liver and plasma. Most zinc transporters are expressed in the small intestine, but Slc39a4 predicts fractional zinc absorption and utilization in young mice.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Materials Science, Multidisciplinary
Bandita Mohapatra, Nimisha Sharma
Summary: Biosynthesized Ag-ZnO nanohybrids were characterized using various techniques and were found to have significant antifungal activity against Schizosaccharomyces pombe. It was discovered that the antifungal action of these nanohybrids is mainly due to the generation of reactive oxygen species (ROS), which leads to oxidative stress, lipid peroxidation, and cell damage. These findings provide insights into the mechanism of action and potential applications of Ag-ZnO nanohybrids for antifungal purposes.
MATERIALS TODAY COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jie Zhao, Sijie Liu, Clemens Alexander Wolf, Gerhard Wolber, Maria Kristina Parr, Matthias Bureik
Summary: Alprazolam, a commonly used drug for managing anxiety disorders, is metabolized by CYP3A enzymes. This study compared the metabolism of alprazolam by all four human CYP3A enzymes and found that CYP3A4 and CYP3A5 have the highest production rates of 4-hydroxyalprazolam, while CYP3A5 alone is the major producer of alpha-hydroxyalprazolam. Computational simulations explained the difference in preferred oxidation sites between CYP3A5 and CYP3A43. Unexpectedly, three CYP3A43 mutants produced a different metabolite, 5-N-O alprazolam. The mutants also showed higher production rates of 4-hydroxyalprazolam compared to the wild-type, while the wild-type did not produce 5-N-O alprazolam.
Article
Biochemistry & Molecular Biology
Kim Kiat Lim, Hwei Yee Teo, Yuan Yee Tan, Yi Bing Zeng, Ulysses Tsz Fung Lam, Mahesh Choolani, Ee Sin Chen
Summary: MTHFR is a key enzyme in the folate metabolic pathway, linked to various human conditions. The fission yeast gene met11(+) shows similar function to MTHFR, affecting chromosome stability and meiotic fidelity. Cooperation among Met11, Rec8, and Sgo1 is crucial for proper genetic inheritance during mitosis and meiosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ying-Ying Wang, Jianxiu Zhang, Xiao-Man Liu, Yulu Li, Jianhua Sui, Meng-Qiu Dong, Keqiong Ye, Li-Lin Du
Summary: This study uncovers the mechanism of how a receptor called Nbr1 in fission yeast recognizes specific protein cargos, revealing the mechanism of autophagy cargo recognition. The research shows that Nbr1-ZZ1 can not only recognize the N-termini of cargos via a conserved acidic pocket, but also engage other parts of the cargos in a cargo-specific manner.
Article
Biochemistry & Molecular Biology
Kim Kiat Lim, Nathaniel Zhi Hao Koh, Yi Bing Zeng, Jun Kai Chuan, Raechell Raechell, Ee Sin Chen
Summary: Our study identified that disruption of membrane transport, chromosome segregation, and mitochondrial oxidative phosphorylation increase cellular susceptibility towards 5-FU, while null mutants of Ino80 complex factors exhibit resistance. Modulating the function of Ino80 complex factors may potentially reverse 5-FU resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Miriam Sanso, Pabitra K. Parua, Daniel Pinto, J. Peter Svensson, Viviane Pag, Danny A. Bitton, Sarah MacKinnon, Patricia Garcia, Elena Hidalgo, Jurg Bahler, Jason C. Tanny, Robert P. Fisher
NUCLEIC ACIDS RESEARCH
(2020)
Article
Geriatrics & Gerontology
Charalampos Rallis, Michael Muelleder, Graeme Smith, Yan Zi Au, Markus Ralser, Jurg Bahler
Summary: Research shows that changes in amino acid levels can affect the lifespan of nondividing yeast cells during aging, specifically with glutamine decreasing in wild-type cells and aspartate increasing in pka1 mutant cells. Supplementation of certain amino acids can either extend or shorten cellular lifespan.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani Garapati, Steven J. Marygold, Vitor Trovisco, Gil Dos Santos, Kathleen Falls, Christopher Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodriguez-Lopez, Marcio L. Acencio, Martin Kuiper, Astrid Laegreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus Chibucos, Michelle Giglio, Suvarna Nadendla, James Munro, Rebecca Jackson, Margaret J. Duesbury, Noemi Del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert Daniel Finn, Alexander Lawson Mitchell, Neil David Rawlings, Lorna Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jurg Bahler, Elizabeth R. Bolton, Jeffery L. De Pons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek A. Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea Auchincloss, Kristian Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria J. Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Sandra Orchard, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos N. Chan, Christian Grove, Raymond Y. N. Lee, Hans-Michael Muller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser
Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.
NUCLEIC ACIDS RESEARCH
(2021)
Correction
Multidisciplinary Sciences
Christopher J. Minnis, StJohn Townsend, Julia Petschnigg, Elisa Tinelli, Juerg Baehler, Claire Russell, Sara E. Mole
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
David A. Ellis, Felix Reyes-Martin, Maria Rodriguez-Lopez, Cristina Cotobal, Xi-Ming Sun, Quentin Saintain, Daniel C. Jeffares, Samuel Marguerat, Victor A. Tallada, Jurg Bahler
Summary: Aberrant repair of DNA double-strand breaks can lead to chromosomal rearrangements, particularly during the aging process. Accumulation of DNA breakpoint junctions with age is associated with microhomology sequences and R-loops. Genome rearrangements in old cells may be driven by age-associated changes in RNA-binding proteins, resulting in non-random patterns of chromosomal rearrangements.
Article
Cell Biology
Catalina A. Romila, StJohn Townsend, Michal Malecki, Stephan Kamrad, Maria Rodriguez-Lopez, Olivia Hillson, Cristina Cotobal, Markus Ralser, Jurg Bahler
Summary: Ageing-related processes are largely conserved, with yeast cells providing an effective model system for studying cellular ageing. By decoding barcodes and using barcode sequencing methods, many new ageing-associated genes were successfully identified.
Article
Multidisciplinary Sciences
Carina C. Kern, StJohn Townsend, Antoine Salzmann, Nigel B. Rendell, Graham W. Taylor, Ruxandra M. Comisel, Lazaros C. Foukas, Jurg Bahler, David Gems
Summary: The study shows that post-reproductive C. elegans mothers vent yolk to support offspring growth, resembling a form of lactation, providing new insights into their rapid senescence. Furthermore, this process is regulated by the insulin/IGF-1 signaling pathway.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Maria Rodriguez-Lopez, Shajahan Anver, Cristina Cotobal, Stephan Kamrad, Michal Malecki, Clara Correia-Melo, Mimoza Hoti, StJohn Townsend, Samuel Marguerat, Sheng Kai Pong, Mary Y. Wu, Luis Montemayor, Michael Howell, Markus Ralser, Jurg Bahler
Summary: This study systematically analyzed the cellular roles of lincRNAs in Schizosaccharomyces pombe, revealing that most lincRNAs exert cellular functions in specific environmental or physiological contexts.
Correction
Biology
Maria Rodriguez-Lopez, Shajahan Anver, Cristina Cotobal, Stephan Kamrad, Michal Malecki, Clara Correia-Melo, Mimoza Hoti, StJohn Townsend, Samuel Marguerat, Sheng Kai Pong, Mary Y. Wu, Luis Montemayor, Michael Howell, Markus Ralser, Jurg Bahler
Article
Genetics & Heredity
Midori A. Harris, Kim M. Rutherford, Jacqueline Hayles, Antonia Lock, Jurg Bahler, Stephen G. Oliver, Juan Mata, Valerie Wood
Summary: PomBase is a model organism database for the fission yeast Schizosaccharomyces pombe, serving the research community within and beyond by providing comprehensive data collections and intuitive displays of genetic, molecular, and cell biological knowledge. It also promotes innovation in the field of model organism databases through new content, advanced query capabilities, and biologist-friendly data summaries and visualization.
Article
Multidisciplinary Sciences
Lidia Lipinska-Zubrycka, Maciej Grochowski, Jurg Bahler, Michal Malecki
Summary: Messenger RNA uridylation is widespread in eukaryotes, and using a simple bioinformatics approach, the presence of uridylation marks in fission yeast was detected. The study confirmed the role of the uridyltransferases Cid1 and Cid16 in mRNA uridylation in fission yeast.
Article
Microbiology
Stephan Kamrad, Clara Correia-Melo, Lukasz Szyrwiel, Simran Kaur Aulakh, Juerg Baehler, Vadim Demichev, Michael Muelleder, Markus Ralser
Summary: We developed a proteomics-based technology called differential isotope labeling by amino acids (DILAC) that can detect producer and consumer subpopulations within an isogenic cell population. By deconvoluting their proteomes using DILAC, we found evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. By combining DILAC with fluorescence-activated cell sorting, we showed that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B.
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Matthias Weith, Jan Grossbach, Mathieu Clement-Ziza, Ludovic Gillet, Maria Rodriguez-Lopez, Samuel Marguerat, Christopher T. Workman, Paola Picotti, Jurg Baehler, Ruedi Aebersold, Andreas Beyer
Summary: The complexity of cellular and organismal traits is a result of the integration of genetic and environmental factors through molecular networks. While the structure and propagation of effects in networks are best understood at the level of functional modules, there is currently no established concept to include the global network state.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biology
Maria Rodriguez-Lopez, Nicola Bordin, Jon Lees, Harry Scholes, Shaimaa Hassan, Quentin Saintain, Stephan Kamrad, Christine Orengo, Juerg Baehler
Summary: This study utilized phenomics and machine-learning approaches to uncover broad cues on protein functions through research on a yeast species. It successfully identified novel protein functions and made predictions for protein functions using phenotype-correlation networks and machine learning methods. Experimental validation demonstrated the accuracy of the predictions, highlighting the importance of these findings in uncovering new protein functions.
Article
Genetics & Heredity
Manuel Lera-Ramirez, Jurg Bahler, Juan Mata, Kim Rutherford, Charles S. Hoffman, Sarah Lambert, Snezhana Oliferenko, Sophie G. Martin, Kathleen L. Gould, Li-Lin Du, Sarah A. Sabatinos, Susan L. Forsburg, Olaf Nielsen, Paul Nurse, Valerie Wood
Summary: Standardized nomenclature for genes, gene products, and isoforms is crucial for clear communication and efficient sharing of scientific data. This publication extends the fission yeast clade gene nomenclature guidelines to support curation efforts at PomBase, introducing guidelines for noncoding RNA genes and updating allele and genotype nomenclature. Adoption of these rules will improve consistency in gene and genotype nomenclature and enhance machine-readability in publications or datasets.